Question: Bowtie2 code help
0
gravatar for sghoshucla
3.1 years ago by
sghoshucla0
sghoshucla0 wrote:

Hi I am new to RNA seq analysis. I am trying to run bowtie2 in command line but failed. can somebody help with the code

qsub -l h_data=4G,time=2:00:00 -cwd -b y ‘module load bowtie2; bowtie2 -p 4 -x Bowtie2Index -1N704.fastq -S bowtie.N704’

also I would like to know if I can get a separate file for unaligned reads.

thanks

rna-seq • 961 views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by sghoshucla0
1

Try -U rather than -1 and make sure it has a space after it. Also, if a command "fails", it helps if you describe in what way it fails and whether you get an error message...

ADD REPLYlink written 3.1 years ago by Devon Ryan90k

Thanks Eagle Eye and Devon Ryan. I have one more question. I am analyzing samples from yeast. should I use jut BowtieIndex or something else? also, I would like to know whether I can get the reads that are not aligned.

thanks

ADD REPLYlink written 3.1 years ago by sghoshucla0
1

Use bowtie2index for yeast genome.
Check the --un and --un-conc options for bowtie2. That should allow you to collect reads that don't align into a file.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax68k
2
gravatar for EagleEye
3.1 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

If you say RNAseq analysis, bowtie is not a good idea. Use some splice aware aligner like Tophat, STAR, GSNAP or SOAP-splice.

Answer to the command: try with -U

bowtie2 -p 4 -x Bowtie2Index -U N704.fastq -S bowtie.N704

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by EagleEye6.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2158 users visited in the last hour